Molgera is the second of the two monsters guarding the power of the sages that can restore the true Master Sword. Together with Jalhalla he was created a long time ago by Ganondorf himself. Molgera lives deep down in the Wind Temple and he is the one who guards the power of Fado, the sage of wind, who he killed ages earlier at the time when Ganondorf weakened the Master Sword.
When you have entered the chamber, jump down into the sand and roll straight forward to trigger the cut scene.
To beat Molgera you will need the dungeon item, the Hookshot. Right when the fight starts Molgera will be under the sand. After a few seconds his head will come up, and with a good aim you can hook his tongue before it is fully arisen.
The first part of this fight, or the first phase actually, is pretty casual and all you need to do is hook his tongue and slash it with your sword. The best way to deliver damage with your sword is with the use quick spins. But do notice, even though Molgera has the solid 12 HP, double damage from the elixir soup has no effect what so ever on the amount of damage he takes. In fact, Molgera does actually only lose 1 HP of each hit he takes, meaning that a quick spin takes 2 HP in damage due to the double hit it delivers.
In each of the four cycles you need to deliver three hits before the next cycle begins. This means that you actually need to deliver 12 hits before Molgera is defeated, and the fight can not be done in less than four cycles. After the first cycle, where Molgera has been hooked in the sand, he will hide under the sand and come back up beneath you a few moments later. Repeat the first cycle once more.
By getting storage before the fight starts, you can keep the storage all the way to the boss defeat cutscene. After starting the molgera intro cutscene, go on the platform and wait. You will fall OoB and fall onto an OoB platform very far underground. Don't move and wait for Molgera to eat you to teleport back up. This way you will be able to fight Molgera while still having storage. This allows you to pick up the heart container during the cutscene in 100% to skip the defeat cutscene and save 40s. In other categories, this can allow you to go into the portal during the cutscene to save a little bit of time.
It is possible to skip all phases of molgera. After the second hit of each phase, if you hookshot the tongue, then have it get hit, then hookshot it again (frame perfect) you can renew the next phase immediately.
After 6 HP has been taken from Molgera, he will begin a new phase of the fight. Soon you will face this giant sand worm rush himself out if the sand and fly above you in the chamber. In this phase, Molgera will dive towards you and this is where the interesting strategies takes part. If you manually target towards the middle of Molgera's open mouth, you will notice that the hitbox of his tongue still exists. This means, that even though Molgera's tongue isn't outside of his moth and he is diving in full speed against you, you can hook him up and deliver damage corresponding 3 HP once again. After this is done, Molgera will repeat just the same thing once more. Hook his tongue in the air once more, and finish him off!
If you manage to get the first air snipe, it is possible to grab her tongue a second time before she dives under the ground. You should aim your hookshot between the gills and fire the hookshot when your reticule is aligned with the 2nd gill. There is a four frame window to successfully grab the tongue, assuming you never move the reticule downward.
For three versions of this game, the NTSC-J version (which means, the Japanese version) and the European or Australian PAL versions, beating Molgera with the strategies we described for the second phase can actually crash the game. What causes this is still not completely determined, but as far as we have seen it, it seems to be linked with the way you finishes him off. Without any actually real proof that this is correct, you usually avoid finishing him off with the use of quick spins, and instead you kill him with normal slashes.
You will know that the crash is about to happen if the victory music at the end of Molgera's death animation does not play.
For some reason, this crash has still not been proven to happen in the NTSC version of the game.